RetrogeneDB ID: retro_shar_237

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834736.1:1327773..1328064(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000013831
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CETN1
• Ensembl ID: ENSSHAG00000015319
• Aliases: None
• Description: centrin, EF-hand protein, 1 [Source:HGNC Symbol;Acc:1866]

Sequence

>retro_shar_237
ATATCTGACCTTGACAAGGAGGGGATAGAGAAAATGAGTTTCTTGGCAATGATGACTCAAAAAATGGTTGAAAAGGATAC
CAAAGAAGAAATTATGAAGGCTTTAATACTCTTCAATGATGATGAAACTAGAAAAACTTCCTTCAAGAATTTAAAACATG
TGGCTAGAAAGCTAGGAGAAAAGTTAATTGATGAGGAACTACAGGAAATAATTGACAAAGCCGATCAAGATGGTGATGGA
GAAATCAATGAACAGGAATTCCCGCAGATCATGAAAAAGATCAATCTGTAT

Alignment

ORF - retro_shar_237 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 54.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISDIDKEGTGKISFNDFLAVMTQKMAEKDTREEILKAFRLFDDDETGKISFKNLKRVARELGENLTDEEL
          ISD.DKEG..K.S...FLA.MTQKM.EKDT.EEI.KA..LF.DDET.K.SFKNLK.VAR.LGE.L.DEEL
Retrocopy ISDLDKEGIEKMS---FLAMMTQKMVEKDTKEEIMKALILFNDDETRKTSFKNLKHVARKLGEKLIDEEL

Parental  QEMIDEADRDGDGEVNEQEFLRIMKKTSLY
          QE.ID.AD.DGDGE.NEQEF..IMKK..LY
Retrocopy QEIIDKADQDGDGEINEQEFPQIMKKINLY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_237 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013823	2 retrocopies	retro_meug_1093, retro_meug_856,
Monodelphis domestica	ENSMODG00000005932	1 retrocopy	retro_mdom_87,
Sarcophilus harrisii	ENSSHAG00000015319	2 retrocopies	retro_shar_237 , retro_shar_378,